GeneNetworkBuilder: Build Regulatory Network from ChIP-chip/ChIP-seq and Expression Data
Version 1.18.1

Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.

AuthorJianhong Ou , Haibo Liu, Heidi A Tissenbaum and Lihua Julie Zhu
Bioconductor views GraphAndNetwork Microarray Sequencing
Date of publicationNone
MaintainerJianhong Ou <jianhong.ou@umassmed.edu>
LicenseGPL (>= 2)
Version1.18.1
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("GeneNetworkBuilder")

Getting started

Package overview
GeneNetworkBuilder Guide
Working with BioGRID, STRING

Popular man pages

ce.IDsMap: C.elegns gene name to wormbase identifier map
ce.mapIDs: map file for converting from wormbase identifier to...
example.data: example datasets for documentation
hs.mapIDs: map file for converting from Entrez identifier to _Homo...
hs.miRNA.map: micro RNA of _Homo sapiens_
polishNetwork: generate an object of grahpNEL to represent the regulation...
saveXGMML: Save network as xgmml
See all...

All man pages Function index File listing

Man pages

browseNetwork: browse network
browseNetwork-shiny: Shiny bindings for browseNetwork
buildNetwork: construct the regulatory network
ce.IDsMap: C.elegns gene name to wormbase identifier map
ce.interactionmap: transcript regulatory map of _Caenorhabditis elegans_
ce.mapIDs: map file for converting from wormbase identifier to...
ce.miRNA.map: micro RNA of _Caenorhabditis elegans_
convertID: convert gene IDs by id map
example.data: example datasets for documentation
exportNetwork: Save network in various formats
filterNetwork: filter the regulatory network table by expression profile
GeneNetworkBuilder-package: Build Regulatory Network from ChIP-chip/ChIP-seq and...
hs.IDsMap: map file for converting gene name or sequence name of _Homo...
hs.interactionmap: transcript regulation map of _Homo sapiens_
hs.mapIDs: map file for converting from Entrez identifier to _Homo...
hs.miRNA.map: micro RNA of _Homo sapiens_
polishNetwork: generate an object of grahpNEL to represent the regulation...
saveXGMML: Save network as xgmml
uniqueExprsData: unique the microarray data

Functions

GeneNetworkBuilder Man page
GeneNetworkBuilder-package Man page
browseNetwork Man page Source code
browseNetwork-shiny Man page
browseNetworkOutput Man page Source code
buildNetwork Man page Source code
ce.IDsMap Man page
ce.interactionmap Man page
ce.mapIDs Man page
ce.miRNA.map Man page
checkCName Source code
checkMCName Source code
checkMap Source code
checkmiRNAmap Source code
convertID Man page Source code
example.data Man page
exportNetwork Man page Source code
filterNetwork Man page Source code
getMax Source code
getMedian Source code
getMin Source code
hs.IDsMap Man page
hs.interactionmap Man page
hs.mapIDs Man page
hs.miRNA.map Man page
inList Source code
polishNetwork Man page Source code
renderBrowseNetwork Man page Source code
saveXGMML Man page Source code
uniqueExprsData Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/GeneNetworkBuilder.R
R/applications.R
R/browseNetwork.R
R/dataset.R
R/exportNetwork.R
R/networkBuilder.R
build
build/vignette.rds
data
data/ce.IDsMap.rda
data/ce.interactionmap.rda
data/ce.mapIDs.rda
data/ce.miRNA.map.rda
data/datalist
data/example.data.rda
data/hs.IDsMap.rda
data/hs.interactionmap.rda
data/hs.mapIDs.rda
data/hs.miRNA.map.rda
inst
inst/doc
inst/doc/GeneNetworkBuilder_vignettes.R
inst/doc/GeneNetworkBuilder_vignettes.Rmd
inst/doc/GeneNetworkBuilder_vignettes.html
inst/doc/with.BioGRID.STRING.R
inst/doc/with.BioGRID.STRING.Rmd
inst/doc/with.BioGRID.STRING.html
inst/htmlwidgets
inst/htmlwidgets/browseNetwork.js
inst/htmlwidgets/browseNetwork.yaml
inst/htmlwidgets/lib
inst/htmlwidgets/lib/cytoscape
inst/htmlwidgets/lib/cytoscape/cytoscape.min.js
inst/htmlwidgets/lib/exportbox
inst/htmlwidgets/lib/exportbox/cytoscape-exportbox.css
inst/htmlwidgets/lib/exportbox/cytoscape-exportbox.js
inst/htmlwidgets/lib/fontawesome
inst/htmlwidgets/lib/fontawesome/css
inst/htmlwidgets/lib/fontawesome/css/font-awesome.css
inst/htmlwidgets/lib/fontawesome/css/font-awesome.min.css
inst/htmlwidgets/lib/fontawesome/fonts
inst/htmlwidgets/lib/fontawesome/fonts/FontAwesome.otf
inst/htmlwidgets/lib/fontawesome/fonts/fontawesome-webfont.eot
inst/htmlwidgets/lib/fontawesome/fonts/fontawesome-webfont.svg
inst/htmlwidgets/lib/fontawesome/fonts/fontawesome-webfont.ttf
inst/htmlwidgets/lib/fontawesome/fonts/fontawesome-webfont.woff
inst/htmlwidgets/lib/fontawesome/fonts/fontawesome-webfont.woff2
inst/htmlwidgets/lib/fontawesome/less
inst/htmlwidgets/lib/fontawesome/less/animated.less
inst/htmlwidgets/lib/fontawesome/less/bordered-pulled.less
inst/htmlwidgets/lib/fontawesome/less/core.less
inst/htmlwidgets/lib/fontawesome/less/fixed-width.less
inst/htmlwidgets/lib/fontawesome/less/font-awesome.less
inst/htmlwidgets/lib/fontawesome/less/icons.less
inst/htmlwidgets/lib/fontawesome/less/larger.less
inst/htmlwidgets/lib/fontawesome/less/list.less
inst/htmlwidgets/lib/fontawesome/less/mixins.less
inst/htmlwidgets/lib/fontawesome/less/path.less
inst/htmlwidgets/lib/fontawesome/less/rotated-flipped.less
inst/htmlwidgets/lib/fontawesome/less/screen-reader.less
inst/htmlwidgets/lib/fontawesome/less/stacked.less
inst/htmlwidgets/lib/fontawesome/less/variables.less
inst/htmlwidgets/lib/fontawesome/scss
inst/htmlwidgets/lib/fontawesome/scss/_animated.scss
inst/htmlwidgets/lib/fontawesome/scss/_bordered-pulled.scss
inst/htmlwidgets/lib/fontawesome/scss/_core.scss
inst/htmlwidgets/lib/fontawesome/scss/_fixed-width.scss
inst/htmlwidgets/lib/fontawesome/scss/_icons.scss
inst/htmlwidgets/lib/fontawesome/scss/_larger.scss
inst/htmlwidgets/lib/fontawesome/scss/_list.scss
inst/htmlwidgets/lib/fontawesome/scss/_mixins.scss
inst/htmlwidgets/lib/fontawesome/scss/_path.scss
inst/htmlwidgets/lib/fontawesome/scss/_rotated-flipped.scss
inst/htmlwidgets/lib/fontawesome/scss/_screen-reader.scss
inst/htmlwidgets/lib/fontawesome/scss/_stacked.scss
inst/htmlwidgets/lib/fontawesome/scss/_variables.scss
inst/htmlwidgets/lib/fontawesome/scss/font-awesome.scss
inst/htmlwidgets/lib/jquery
inst/htmlwidgets/lib/jquery/jquery.min.js
inst/htmlwidgets/lib/panzoom
inst/htmlwidgets/lib/panzoom/cytoscape-panzoom.js
inst/htmlwidgets/lib/panzoom/cytoscape.js-panzoom.css
inst/htmlwidgets/lib/qtip2
inst/htmlwidgets/lib/qtip2/cytoscape-qtip.js
inst/htmlwidgets/lib/qtip2/jquery.qtip.min.css
inst/htmlwidgets/lib/qtip2/jquery.qtip.min.js
inst/htmlwidgets/lib/searchbox
inst/htmlwidgets/lib/searchbox/cytoscape-searchbox.css
inst/htmlwidgets/lib/searchbox/cytoscape-searchbox.js
inst/unitTests
inst/unitTests/test_geneNetworkBuilder.R
man
man/GeneNetworkBuilder-package.Rd
man/browseNetwork-shiny.Rd
man/browseNetwork.Rd
man/buildNetwork.Rd
man/ce.IDsMap.Rd
man/ce.interactionmap.Rd
man/ce.mapIDs.Rd
man/ce.miRNA.map.Rd
man/convertID.Rd
man/example.data.Rd
man/exportNetwork.Rd
man/filterNetwork.Rd
man/hs.IDsMap.Rd
man/hs.interactionmap.Rd
man/hs.mapIDs.Rd
man/hs.miRNA.map.Rd
man/polishNetwork.Rd
man/saveXGMML.Rd
man/uniqueExprsData.Rd
src
src/Makevars
src/Makevars.win
src/geneTree.cpp
src/geneTree.h
src/nodefilter.cpp
tests
tests/runTests.R
vignettes
vignettes/GeneNetworkBuilder_vignettes.Rmd
vignettes/bibliography.bib
vignettes/nature.csl
vignettes/with.BioGRID.STRING.Rmd
vignettes/workflow.png
GeneNetworkBuilder documentation built on May 20, 2017, 11:03 p.m.

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